|
| Status |
Public on Apr 24, 2024 |
| Title |
585B1 BTAG TET1 KO#2 |
| Sample type |
SRA |
| |
|
| Source name |
585B1 BTAG
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 585B1 BTAG
cell type: human iPSC
genotype: TET1 KO#2
treatment: Expansion culture with BMP signalling
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was integrated in "library construction protocol" process.
Whole-cell suspensions harvested from the expansion culture were pelleted and were subjected to Cell Multiplexing Oligo labeling. Alternatively, samples for analysis were cryopreserved as follows: whole-cell suspensions harvested from the expansion culture were pelleted and were resuspended in Cell Banker Type 1 Plus for cryopreservation at −80˚C. For Cell Multiplexing Oligo labeling, after thawing in the water bath at 37℃ if needed, collected cells were resuspended in Cell Multiplexing Oligo solution and were incubated for 5 minutes at room temperature. After the incubation, cells were washed with 1% BSA (SIGMA, A1519)-PBS (−) and were collected by centrifugation at 200g for 10 minutes. Collected cells were resuspended in 1% BSA-PBS (−) containing anti-TRA-1-85 antibody (BD Bioscience, 563302, 1:20) and placed on ice for 30 minutes in the dark. Then, the cells were washed with PBS once and were resuspended in 1% BSA-PBS (−) containing 3 μM DRAQ7 (abcam, ab109202). To isolate live human cells, TRA-1-85 (+) DRAQ7(−) cells were sorted into DMEM/F12 (GIBCO, 10565-018) + 1% BSA by FACS Aria III. Sorted cells were subjected to the subsequent library construction using 10X Genomics Single Cell 3’ Kit v. 3.1, followed by sequencing on an Illumina NovaSeq 6000 platform. All steps were performed in accordance with the manufacturer's instructions.
scRNAseq(10X Genomics Single Cell 3’ Kit v. 3.1)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
585B1 BTAG TET1 KO#2 hPGCLC BMP2-driven differentiation c18
|
| Data processing |
Read data generated from samples labeled with Cell Multiplexing Oligo were processed with cellranger v6.0.1 with “multi” option.
Assembly: GRCh38.p12
|
| |
|
| Submission date |
May 05, 2023 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Yukihiro Yabuta |
| E-mail(s) |
yabyab@anat2.med.kyoto-u.ac.jp
|
| Organization name |
Kyoto University, Graduate school of medicine
|
| Department |
Anatomy and Cell Biology
|
| Street address |
Yoshida-Konoe-cho, Sakyo-ku
|
| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE231812 |
In vitro reconstitution of epigenetic reprogramming in the human germ line [10X] |
| GSE232078 |
In vitro reconstitution of epigenetic reprogramming in the human germ line |
|
| Relations |
| BioSample |
SAMN34720754 |
| SRA |
SRX20238288 |
